NM_017582.7:c.537+232G>A

Variant names:

• chr1-154555196-C-T
• rs7543174
• NM_017582.7:c.537+232G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017582.7(UBE2Q1):​c.537+232G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,152 control chromosomes in the GnomAD database, including 44,599 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.76 (44599 hom., cov: 32)
• Consequence: UBE2Q1 NM_017582.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 16 publications found

Genes affected

UBE2Q1 (HGNC:15698): (ubiquitin conjugating enzyme E2 Q1) The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin-protein ligases (E3s). This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. The encoded protein is 98% identical to the mouse counterpart. [provided by RefSeq, Jul 2008]

UBE2Q1-AS1 (HGNC:40722): (UBE2Q1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE2Q1	NM_017582.7	c.537+232G>A		intron_variant	Intron 3 of 12	ENST00000292211.5	NP_060052.3
UBE2Q1	XM_047424467.1	c.537+232G>A		intron_variant	Intron 3 of 11		XP_047280423.1
UBE2Q1-AS1	NR_046668.1	n.*168C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBE2Q1	ENST00000292211.5	c.537+232G>A		intron_variant	Intron 3 of 12	1	NM_017582.7	ENSP00000292211.4

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115280 AN: 152034 Hom.: 44573 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.790

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.758 AC: 115349 AN: 152152 Hom.: 44599 Cov.: 32 AF XY: 0.762 AC XY: 56706 AN XY: 74380

African (AFR) AF: 0.591 AC: 24513 AN: 41480

American (AMR) AF: 0.812 AC: 12413 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2782 AN: 3470

East Asian (EAS) AF: 0.878 AC: 4540 AN: 5172

South Asian (SAS) AF: 0.833 AC: 4011 AN: 4818

European-Finnish (FIN) AF: 0.834 AC: 8837 AN: 10596

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55623 AN: 68008

Other (OTH) AF: 0.788 AC: 1665 AN: 2112

Alfa AF: 0.807 Hom.: 41639

Bravo AF: 0.750

Asia WGS AF: 0.804 AC: 2797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.60
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7543174; hg19: chr1-154527672;